MolNFT v1 · #137059 · protein
Structure of alpha-galactosylphytosphingosine bound by CD1D and in complex with the VA14VB8.2 TCR
5VCJ · Antigen-presenting glycoprotein CD1D1: “Structure of alpha-galactosylphytosphingosine bound by CD1D and in complex with the VA14VB8.2 TCR”. X-ray diffraction, 6 ligands (N57, PLM, NAG), 8 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 5VCJ
- Type
- protein
- Length
- 805 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin; Chimeric TCR…
- UniProt
- P11609, P01887, A0A0B4J1J9, K7N5M3
- Ligands
- N57, PLM, NAG, MAN, BMA, FUC
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 267 | 26% helix, 41% strand | P11609 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P01887 |
| C | Chimeric TCR VALPHA14/JALPHA18 chain (mouse variable domain, human constant domain) | protein | 201 | 1% helix, 48% strand | A0A0B4J1J9, K7N5M3 |
| D | Chimeric TCR VBETA8.2 chain (mouse variable domain, human constant domain) | protein | 239 | 6% helix, 48% strand | — |
Ligands and binding sites
- N57 · (2S,3S,4R)-2-amino-3,4-dihydroxyoctadecyl alpha-D-galactopyranoside · ligand · chains A, C
- PLM · Palmitic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 926 | 0.86 | 0.87 | 78 | N57, PLM |
| 2 | 986 | 0.71 | 0.75 | 75 | empty |
| 3 | 420 | 0.67 | 0.79 | 43 | empty |
| 4 | 191 | 0.49 | 0.76 | 31 | empty |
| 5 | 123 | 0.45 | 0.78 | 30 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2116 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1240 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 474 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 364 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5VCJ · Structure of alpha-galactosylphytosphingosine bound by CD1d and in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
- P11609 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D1 (P11609) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P11609
- Every structure of UniProt P01887
- Every structure of UniProt A0A0B4J1J9
- Every structure of UniProt K7N5M3
- Elsewhere: RCSB PDB 5VCJ · PDBe 5VCJ · UniProt P11609 · UniProt P01887 · UniProt A0A0B4J1J9 · UniProt K7N5M3
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